7OMX

Thermus sp. 2.9 DarT in complex with carba-NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OMVD_1292116023

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29464 mM potassium thiocyanate, 20% (w/v) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
2.1943.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.034α = 90
b = 71.282β = 90
c = 85.542γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5254.7799.30.10.1090.0430.9978.8633587
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.521.560.9321.0720.5140.5811.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUED_12921160231.5242.77133520164299.1390.1750.17330.202718.143
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.1151.0530.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.206
r_dihedral_angle_4_deg15.148
r_dihedral_angle_3_deg12.444
r_dihedral_angle_1_deg6.775
r_lrange_it4.43
r_lrange_other4.242
r_scangle_it2.195
r_scangle_other2.171
r_angle_refined_deg1.53
r_scbond_it1.433
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.206
r_dihedral_angle_4_deg15.148
r_dihedral_angle_3_deg12.444
r_dihedral_angle_1_deg6.775
r_lrange_it4.43
r_lrange_other4.242
r_scangle_it2.195
r_scangle_other2.171
r_angle_refined_deg1.53
r_scbond_it1.433
r_mcangle_it1.418
r_mcangle_other1.418
r_scbond_other1.379
r_angle_other_deg1.356
r_mcbond_it0.874
r_mcbond_other0.872
r_symmetry_xyhbond_nbd_refined0.218
r_nbd_other0.215
r_symmetry_nbd_refined0.214
r_nbd_refined0.195
r_nbtor_refined0.181
r_symmetry_nbd_other0.177
r_xyhbond_nbd_other0.166
r_xyhbond_nbd_refined0.14
r_symmetry_nbtor_other0.082
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1607
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing